ArticleGenome research2019
Interplay between coding and exonic splicing regulatory sequences.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 18 citations in OpenAlex.
- Evaluating splicing factor and kinase network crosstalk through global phosphoproteomics.bioRxiv : the preprint server for biology · 2026Article
- HSV ICP27 hijacks host splicing factor SRSF3 to regulate pre-mRNA splicing and export for viral gene expression and immune evasion.PLoS pathogens · 2026Article
- Downregulation of Tra2α and Tra2β suppresses lipopolysaccharide-induced inflammation in macrophages by regulating MyD88 mRNA alternative splicing.Molecular and cellular biochemistry · 2026Article
- SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors.Database : the journal of biological databases and curation · 2023Article
- A common intronic single nucleotide variant modifies PKD1 expression level.Clinical genetics · 2022Article
- Myotonic dystrophy RNA toxicity alters morphology, adhesion and migration of mouse and human astrocytes.Nature communications · 2022Article
- Congenital nephrotic syndrome in a Hispanic Guatemalan newborn associated with aBiomedical reports · 2022Article
- Biological function and molecular mechanism of SRSF3 in cancer and beyond.Oncology letters · 2022Review
- SRSF3 Expression Serves as a Potential Biomarker for Prognostic and Immune Response in Pan-Cancer.Frontiers in oncology · 2022Article
- Regulated splicing of large exons is linked to phase-separation of vertebrate transcription factors.The EMBO journal · 2021Article
- The effects of codon bias and optimality on mRNA and protein regulation.Cellular and molecular life sciences : CMLS · 2021Review
- TRA2A-induced upregulation of LINC00662 regulates blood-brain barrier permeability by affecting ELK4 mRNA stability in Alzheimer's microenvironment.RNA biology · 2020Article
- Mutational bias and the protein code shape the evolution of splicing enhancers.Nature communications · 2020Article
- Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.Life (Basel, Switzerland) · 2020Article
- Characterizing the interplay between gene nucleotide composition bias and splicing.Genome biology · 2019Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The inclusion of exons during the splicing process depends on the binding of splicing factors to short low-complexity regulatory sequences. The relationship between exonic splicing regulatory sequences and coding sequences is still poorly understood. We demonstrate that exons that are coregulated by any given splicing factor share a similar nucleotide composition bias and preferentially code for amino acids with similar physicochemical properties because of the nonrandomness of the genetic code. Indeed, amino acids sharing similar physicochemical properties correspond to codons that have the same nucleotide composition bias. In particular, we uncover that the TRA2A and TRA2B splicing factors that bind to adenine-rich motifs promote the inclusion of adenine-rich exons coding preferentially for hydrophilic amino acids that correspond to adenine-rich codons. SRSF2 that binds guanine/cytosine-rich motifs promotes the inclusion of GC-rich exons coding preferentially for small amino acids, whereas SRSF3 that binds cytosine-rich motifs promotes the inclusion of exons coding preferentially for uncharged amino acids, like serine and threonine that can be phosphorylated. Finally, coregulated exons encoding amino acids with similar physicochemical properties correspond to specific protein features. In conclusion, the regulation of an exon by a splicing factor that relies on the affinity of this factor for specific nucleotide(s) is tightly interconnected with the exon-encoded physicochemical properties. We therefore uncover an unanticipated bidirectional interplay between the splicing regulatory process and its biological functional outcome.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.